Variant report

Variant	rs16885998
Chromosome Location	chr6:34268107-34268108
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34266488..34268180-chr6:34270200..34273070,2	MCF-7	breast:
2	chr6:34262225..34265045-chr6:34266800..34268628,2	K562	blood:
3	chr6:34266980..34269551-chr6:34289025..34290920,2	K562	blood:
4	chr6:34263488..34269053-chr6:34269608..34275567,7	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12664001	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12665397	0.85[EUR][1000 genomes]
rs1573905	1.00[CEU][hapmap]
rs16889706	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16889714	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs206919	0.85[CHD][hapmap]
rs206921	0.84[CHD][hapmap]
rs206936	0.83[CHD][hapmap]
rs206941	0.86[JPT][hapmap]
rs206942	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs2071928	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34384951	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3778077	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3798560	0.85[CHD][hapmap]
rs3798562	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3798564	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs410340	0.80[ASN][1000 genomes]
rs464553	0.83[CHD][hapmap]
rs4711390	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713766	1.00[CEU][hapmap]
rs4713770	0.82[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713772	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713773	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4713775	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713776	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4713777	0.87[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs4713780	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4713781	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4713783	0.88[EUR][1000 genomes]
rs4713784	1.00[CEU][hapmap];0.87[MEX][hapmap]
rs4713793	0.91[MEX][hapmap]
rs568502	0.86[JPT][hapmap]
rs58648597	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59310759	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60100381	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs611928	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs6909732	1.00[CEU][hapmap]
rs6912971	0.83[CHD][hapmap]
rs6924682	0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6924982	0.80[ASN][1000 genomes]
rs6925243	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs6930978	0.87[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6935129	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7752035	0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7767431	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9394200	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1798756	chr6:34203406-34319041	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv1798835	chr6:34204183-34319041	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv1792088	chr6:34204285-34318837	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1793127	chr6:34204285-34319041	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	esv1794528	chr6:34267024-34308816	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16885998	RPS10	cis	lymphoblastoid	seeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34240600-34269200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr6:34244400-34273400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:34251000-34283200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:34253600-34271200	Weak transcription	Stomach Mucosa	stomach
5	chr6:34260200-34272800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:34261400-34269000	Weak transcription	NHDF-Ad	bronchial
7	chr6:34261400-34269200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:34261400-34269400	Weak transcription	NHLF	lung
9	chr6:34261400-34273400	Weak transcription	Fetal Kidney	kidney
10	chr6:34261400-34276000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:34261600-34268600	Weak transcription	Brain Substantia Nigra	brain
12	chr6:34261600-34269200	Weak transcription	NH-A	brain
13	chr6:34261600-34269200	Weak transcription	Osteobl	bone
14	chr6:34261600-34273400	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:34261600-34276200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:34261800-34269200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:34261800-34269200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:34261800-34269200	Weak transcription	Brain Germinal Matrix	brain
19	chr6:34261800-34269400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:34261800-34271200	Weak transcription	HUVEC	blood vessel
21	chr6:34261800-34273600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:34261800-34275200	Weak transcription	Aorta	Aorta
23	chr6:34261800-34330800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:34262000-34268200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr6:34262000-34268400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr6:34262000-34269000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:34262000-34269000	Weak transcription	Brain Angular Gyrus	brain
28	chr6:34262000-34269000	Weak transcription	Fetal Lung	lung
29	chr6:34262000-34269200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:34262000-34269200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:34262000-34269200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:34262000-34269200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr6:34262000-34269200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:34262000-34269400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr6:34262000-34274000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:34262000-34276800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:34262000-34282600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr6:34262000-34282800	Weak transcription	Primary T cells from cord blood	blood
39	chr6:34262000-34283400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:34262000-34284600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:34262000-34286600	Weak transcription	Gastric	stomach
42	chr6:34262000-34289000	Weak transcription	Hela-S3	cervix
43	chr6:34262000-34292800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:34262200-34269200	Weak transcription	Adipose Nuclei	Adipose
45	chr6:34262200-34269200	Weak transcription	Ovary	ovary
46	chr6:34262200-34269400	Weak transcription	Liver	Liver
47	chr6:34262200-34273400	Weak transcription	Fetal Brain Female	brain
48	chr6:34262200-34276000	Weak transcription	Pancreas	Pancrea
49	chr6:34262200-34295400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr6:34262200-34301200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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